bpy data out of sync with the actual scene
bpy.data.meshes is all of the meshes in the all of the scenes. Meshes are different from objects, a mesh would be like the vertex positions while an object is made of a mesh, and contains the modifiers, materials, etc. 

If you have an object selected you can see the name of the mesh by going to: Properties Panel &gt; Data here you will see the name of the object's mesh, you can also get a list of all the meshes in the scene.

I am guessing that you have a cube, or an object that at one point was a cube and that is why the mesh name is Cube.

If you want to get rid of meshes that aren't currently being used then you can do something like this

import bpy
for mesh in bpy.data.meshes:
    if mesh.users == 0:
        bpy.data.meshes.remove(mesh)